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Hua-Ying Fan, Ph.D.

Hua-Ying Fan, Ph.D.

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Assistant Professor of Biochemistry and Biophysics
Department: Biochemistry and Biophysics

Contact information
Epigenetics Program
Department of Biochemistry and Biophysics
Perelman School of Medicine
9-133 Smilow Center for Translational Research
3400 Civic Center Blvd
Philadelphia, PA 19104-6059
Office: 215 573-5705
Lab: 215 573-5713
Education:
B.S. (Chemistry)
National Tsing-Hua University, Hsin-Chu, Taiwan, 1989.
M.S. (Chemistry)
New York University, New York, NY, 1990.
Ph.D. (Cellular and Molecular Biology)
Sackler Institute of New York University Medical Center, New York University, New York, NY, 1996.
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Description of Research Expertise

The Fan lab is interested in understanding the mechanisms of epigenetic regulation, focusing on two main directions: (1) the function and regulation of ATP-dependent chromatin remodelers, and (2) the mechanisms of mitotic transcription memory by the retention of sequence-specific transcription factors on mitotic chromatin. Results from these studies will shed light on fundamental mechanisms of epigenetic regulation and provide novel insights into the causes and mechanisms of disease.

ATP-dependent chromatin remodelers make nucleosomal DNA accessible by altering DNA-histone contacts in a non-covalent manner to control fundamental nuclear processes. Thus, these enzymes play critical roles in cell growth, differentiation and development. Aberrant chromatin remodeling activities lead to numerous diseases, including developmental syndromes and cancer, highlighting the importance of these enzymes to human health. The Fan lab has been using the Cockayne syndrome complementation group B protein (CSB) as an experimental paradigm to understand the biochemical properties of remodelers and determine how these activities are utilized in specific biological processes. Currently, the lab is determining how CSB is distinct from other chromatin remodelers and how its unique features equip this enzyme to protect cells from genotoxic stress. Below is a brief summary of recent contributions and achievements of the Fan Lab.

CSB is the only ATP-dependent chromatin remodeler essential for transcription-coupled DNA repair (TCR), a multi-step process that rapidly removes transcription-stalling lesions, such as those created by UV light, to permit the resumption of transcription. The association of CSB with DNA lesion-stalled transcription is the critical first step for initiating TCR. The Fan lab demonstrated that ATP hydrolysis by CSB is essential for stable CSB-chromatin association after UV irradiation and that defects in this association may contribute to Cockayne syndrome. They further identified both positive and negative elements that regulate CSB-chromatin association. They showed that the recruitment of CSB to DNA lesion-stalled transcription requires ATP hydrolysis by CSB to relieve auto-repression mediated by CSB’s N-terminal region. This was the first evidence that ATP-dependent chromatin remodelers not only use ATP as energy to alter chromatin structure, but also to ensure their precise targeting to carry out specific biological functions (Lake et al., Molecular Cell 2010).

The Fan lab has also provided insights into the significance of the poorly understood interaction between CSB and the p53 tumor suppressor (Lake et al., JBC 2011). They demonstrated both in vitro and in cells that CSB can promote the association of p53 with DNA. They proposed that this might serve as a mechanism by which these proteins scan DNA for lesions and coordinate their activities to regulate DNA repair, cell survival, and aging.

It had been a long-standing debate as to whether CSB functions as a classic ATP-dependent chromatin remodeler, since robust chromatin remodeling activity had not been demonstrated for this protein. Using quantitative in vitro remodeling assays, the Fan lab determined that CSB exposes nucleosomal DNA inefficiently, ~20-fold slower than that of other well-characterized chromatin remodeling complexes. Through the identification of CSB-interacting proteins, the Fan lab discovered that robust chromatin remodeling by CSB requires NAP1-like histone chaperones (NAP1L). This finding provided the first example of how the activities of histone chaperones can synergize with ATP-dependent chromatin remodelers to reposition nucleosomes. Additionally, the lab demonstrated that chromatin remodeling by CSB and NAP1L is essential for efficient transcription-coupled DNA repair. In contrast to previous speculations, the Fan lab showed that chromatin remodeling by CSB is not required for the recruitment of the DNA repair machinery but, instead, to make the chromatin environment conducive for efficient DNA repair and/or transcription resumption after repair (Cho, Tsai et al., PLoS Genetics 2013).

Changes in gene expression patterns are associated with loss-of-CSB function, and these changes could account for some of the clinical features of Cockayne syndrome. It had, however, remained unclear whether CSB directly regulates gene expression. The Fan lab provided the first genome-wide map of CSB occupancy, revealing that CSB is enriched at promoters and enhancers. Although CSB does not bind DNA in a sequence-specific manner in vitro, they found that CSB is recruited to specific regions of the genome by the sequence-specific transcription factor c-Jun/AP1, providing the first understanding of the mechanism by which CSB is targeted for transcription regulation. The lab also provided the first direct evidence that CSB does reposition nucleosomes in cells to regulate nearby gene expression (Lake et al, PLoS Genetics 2014).

The Fan lab is also interested in understanding the mechanisms that maintain transcriptional memory through cell division, an important component for cell identity maintenance. They demonstrated that the sequence-specific transcription factor RBPJ, the major transcriptional effector of the Notch signaling pathway, is retained on mitotic chromatin. They also found that sites of RBPJ occupancy are enriched for CTCF-binding motifs, in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates long-range chromatin interactions, these results raise an intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that can be propagated through cell division to maintain specific gene expression programs (Lake, Tsai, et al, PLoS Genetics 2014).

Selected Publications

Lake, R.J., Boetefuer, E.L. Tsai, P.-F., Jeong,J., Choi, I., Won, K.-J., and Fan, H.-Y.: The Sequence-Specific Transcription Factor c-Jun Targets Cockayne Syndrome Protein B to Regulate Transcription and Chromatin Structure. PLoS Genetics 10(4): e1004284, April 2014 Notes: doi:10.1371/journal.pgen.100428.

Lake, R. J., Tsai, P.-F., Choi, I., Won, K.-J., and Fan, H.-Y.: RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin Throughout Mitosis, Suggesting a Role in Mitotic Bookmarking. PLoS Genetics 10(3): e1004204, March 2014.

Cho, I., Tsai, P.-F., Lake, R. J., Basheer, A., and Fan, H.-Y.: ATP-Dependent Chromatin Remodeling by Cockayne Syndrome Protein B and NAP1-like histone chaperones is required for efficient transcription-coupled DNA repair. PLoS Genetics 9(4): e1003407, April 2013.

Lake, R.J. and Fan, H.-Y.: Structure, Function and Regulation of CSB: A Multi-Talented Gymnast. Mechanisms of Ageing and Development. 134(5-6): 202-11, 2013 Notes: Epub 2013 Feb 16.

Lake, R.J., Basheer, A., and Fan, H.-Y.: Reciprocally regulated chromatin association of the Cockayne syndrome protein B and p53. J. Biol. Chem. 286(40): 34951-8, Oct 7 2011 Notes: Epub 2011 Aug 18.

Lake RJ, Geyko A., Hemashettar G., Zhao Y. and Fan, H.-Y. : UV-induced association of the CSB remodeling protein with chromatin requires ATP-dependent relief of N-terminal autorepression. Molecular Cell 37: 235-246, 2010.

Lavigne M, Eskeland R, Azebi S, Saint-André V., Jang, S. M., Batsché,E., Fan, H.-Y., Kingston, R. E., Imhof, A., and Muchardt, C. : Interaction of HP1 and Brg1/Brm with the globular domain of histone H3 required for HP1-mediated repression. PLoS Genetics 5: e1000769. doi:10.1371/journal.pgen.1000769, 2009.

Kelly DF, Lake RJ, Middelkoop TC, Fan H-Y, Artavanis-Tsakonas S, and Waltz, T. : Molecular structure and dimeric organization of the Notch extracellular domain as revealed by electron microscopy. PLoS ONE 5: e10532. doi:10.1371/journal.pone.0010532 2010.

Trotter, K.W., Fan, H.-Y., Ivey, M., Kingston, R.E., Archer, T.K. : The HSA domain of BRG1 mediates critical interactions required for GR2 dependent transcriptional activation in vivo. Mol. Cell Biol. 28: 1413-1426, 2008.

Yu*, A., Fan*, H. -Y., Liao, D., Bailey, A. D. and Weiner, A. M. : Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2 and 5S genes. Molecular Cell 5: 801-810, 2000 Notes: *Co-first author.

Fan, H.-Y., He, X., Kingston, R. E. and Narlikar, G. J. : Distinct strategies to make nucleosomal DNA accessible. Molecular Cell 11: 1311-1322, 2003.

Fan, H.-Y., Trotter, K., Archer, T., and Kingston, R. E. : Swapping function of two chromatin remodeling complexes. Molecular Cell 17: 805-815, 2005.

Dennis, J.H.*, Fan, H.-Y.*, Reynolds, M.S.*, Yuan, G., Meldrim, J, Richter, D.J., Peterson, D.G., Rando, O.J., Noble, W.S., Kingston R.E. : Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res. 17: 928-999, 2007 Notes: *Co-first authorship.

Zhang, Z., Fan, H.-Y., Goldman, J. A., and Kingston, R. E. : Homology driven chromatin remodeling by human Rad54. Nature Struct. Mol. Biol. 14: 397-405, 2007.

He, X., Fan, H.-Y., Garlick, J.D., and Kingston, R.E. : Diverse regulation of SNF2h chromatin remodeling by noncatalytic subunits. Biochemistry 47: 7025-7033, 2008.

Newman, J.C., Bailey, A.D., Fan, H.-Y., Pavelitz, T., and Weiner, A.M. : An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genetics 4: e1000031, 2008.

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Last updated: 07/29/2015
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